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vfonov / mincANTS

Mincified version of PICSL ANTS from http://advants.svn.sourceforge.net/
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Out of memory #1

Open egarza opened 10 years ago

egarza commented 10 years ago

Hi

I am using MagetBrain (https://github.com/CobraLab/MAGeTbrain), which uses mincANTS for registration of subcortical atlases to individual subjects. This is done over at scinet nodes. When I do 20 subjects for this particular sample, I end up with 4 subjects where the registration finished early due to being out of memory. Here I paste an example:

Begin PBS Epilogue Wed Sep 17 19:03:09 EDT 2014 1410994989 Job ID: 25044105.gpc-sched-ib0 Username: egarza Group: mchakrav Job Name: mb_voting_2014-09-17T14:22:55.115166_3 Session: 1497 Limits: neednodes=1:ppn=8,nodes=1:ppn=8,walltime=08:00:00 Resources: cput=32:59:29,mem=12774148kb,vmem=22113664kb,walltime=03:28:01 Queue: batch_ib Account: Nodes: gpc-f128n020-ib0 Killing leftovers... kernel messages produced during job executions:

Things happen and then:

gpc-f128n020-ib0: [ 8154] 3027121 8154 2329 375 4 0 0 bash gpc-f128n020-ib0: [ 8435] 3027121 8435 2326 370 1 0 0 mb_register gpc-f128n020-ib0: [20984] 3027121 20984 617311 337392 8 0 0 mincANTS gpc-f128n020-ib0: [23989] 3027121 23989 2329 375 6 0 0 bash gpc-f128n020-ib0: [24040] 3027121 24040 2326 370 0 0 0 mb_register gpc-f128n020-ib0: [26842] 3027121 26842 698995 419083 4 0 0 mincANTS gpc-f128n020-ib0: [ 5881] 3027121 5881 2329 375 8 0 0 bash gpc-f128n020-ib0: [ 5932] 3027121 5932 2326 370 4 0 0 mb_register gpc-f128n020-ib0: [ 7203] 3027121 7203 367450 87527 3 0 0 mincANTS gpc-f128n020-ib0: [25428] 0 25428 1017 131 4 0 0 sleep gpc-f128n020-ib0: Out of memory: Kill process 26842 (mincANTS) score 102 or sacrifice child gpc-f128n020-ib0: Killed process 26842, UID 3027121, (mincANTS) total-vm:2795980kB, anon-rss:1675368kB, file-rss:964kB gpc-f128n020-ib0: mincANTS invoked oom-killer: gfp_mask=0x280da, order=0, oom_adj=0, oom_score_adj=0 gpc-f128n020-ib0: mincANTS cpuset=/ mems_allowed=0-1 gpc-f128n020-ib0: Pid: 7121, comm: mincANTS Not tainted 2.6.32-358.2.1.el6.x86_64 #1

The registration is done multiple times, therefore reducing the number of registrations should make it work, but it does not work.

I was wondering if someone could point me in the right direction of the problem in mincANTS. I'm reading he code at the moment for both programs, but it would be easier to have somewhere to start.

Thanks in advance

Eduardo

vfonov commented 10 years ago

Perhaps using latest version (which requires ITK 4.6) would solve this problem, I have mincified version in https://github.com/vfonov/ANTs , note that the binary is called just ANTS ( not mincANTS) but it still can produce minc-style xfm files.